What you need to do is to provide an input to exportgraphics to take the figure rather than the axes
When calling exportgraphics with no handle-style input it just exports 'gca' (the last active axes handle)
This should do the trick (using f as the figure handle but you could theoretically just use gcf as your input to exportgraphics)
filename = 'thisisadpdffile.pdf';
x = linspace(-pi*9,pi*9,999);
f = figure;
subplot(2,2,1);
plot(x,sin(x));
subplot(2,2,2);
plot(x,sin(x./2),'color',[155 0 0]/255);
subplot(2,2,[3 4]);
plot(x,cos(x));
hold on
plot(x,1./x);
exportgraphics(f,filename);
